SMTL ID : 9ena.1

Lysosomal glucocerebrosidase in complex with a stabilizing nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: R.2, I.5, N.19, T.21, Y.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.22

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.270

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.235, E.340 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.235, A:E.340, H2O.3, H2O.4, H2O.6, H2O.10 MG.4: 2 residues within 4Å: Chain A: L.317, H.365 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:H.365, H2O.1, H2O.3, H2O.3, H2O.7, H2O.20

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: P.319, A.320, K.321, A.322 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.321, A:A.322 Water bridges: A:T.323 SO4.6: 6 residues within 4Å: Chain A: P.319, A.320, K.321, T.369, Y.373 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.320, A:K.321, A:Y.373 Water bridges: A:A.318 SO4.7: 2 residues within 4Å: Chain A: R.44, S.45 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.44, A:S.45 Salt bridges: A:R.44 SO4.8: 4 residues within 4Å: Chain A: G.193, K.194, S.242, G.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.194, A:G.243 Water bridges: A:K.194, A:S.242 SO4.9: 3 residues within 4Å: Chain A: R.44, S.465, Y.487 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.44 SO4.10: 6 residues within 4Å: Chain A: Y.11, S.12, G.355, S.356, W.357, D.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.12, A:S.13, A:S.356, A:W.357, A:D.358 SO4.11: 4 residues within 4Å: Chain B: A.63, D.64, S.65, R.114 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.64, B:D.64, B:S.65 Water bridges: B:S.65, B:R.114, B:R.114, B:R.114, B:R.114, B:R.114, B:R.114, B:R.114 Salt bridges: B:R.114 SO4.12: 2 residues within 4Å: Chain B: R.102, R.117 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.102, B:R.102 Salt bridges: B:R.102, B:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dal Maso, T. et al., Developing nanobodies as allosteric molecular chaperones of glucocerebrosidase function. Nat Commun (2025)

Release Date

2025-06-04

Peptides

Glucosylceramidase: A
Chains: B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucosylceramidase

Chains: B

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